It sounds like you are trying to render something that has space under it which is hard to do well. But you would need to use the Full 3D options in Step 2 of the uploader to get that to work. That processing is designed for smaller areas though so I would recommend breaking it up into smaller sections.
There are limits to the detail you can render with photogrammetry in general though and you may be getting close to that. Those features are only a couple of pixels wide. You would likely need to get a lot more detail in your images to have those turn out which means flying lower.
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